rs7241142

Positions:

• chr18-894241-G-A
• chr18-894241-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.618 in 151,976 control chromosomes in the GnomAD database, including 31,076 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (31076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93894 AN: 151858 Hom.: 31073 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.618 AC: 93925 AN: 151976 Hom.: 31076 Cov.: 31 AF XY: 0.621 AC XY: 46152 AN XY: 74276

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.649

Alfa AF: 0.663 Hom.: 5874

Bravo AF: 0.610

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7241142; hg19: chr18-894242;